A collection of intrinsic disorder characterizations from eukaryotic proteomes. - database used in this analysis https://www.ncbi.nlm.nih.gov/pubmed/27326998
Molecular signaling involving intrinsically disordered proteins in prostate cancer. https://www.ncbi.nlm.nih.gov/pubmed/27212129
Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites. https://www.ncbi.nlm.nih.gov/pubmed/27332813
Intrinsically Disordered Side of the Zika Virus Proteome. https://www.ncbi.nlm.nih.gov/pubmed/27867910
Origin of a folded repeat protein from an intrinsically disordered ancestor. https://www.ncbi.nlm.nih.gov/pubmed/27623012
Species to select from: “Homo sapiens”, “Mus musculus”, “strain ATCC 204508”, “strain K12” Paste value in the code chunk below
all Uniprot if reviewed == 1, only Swissprot data if reviewed == 2, TrEMBL data if reviewed == 3 only reviewed = 2 is relevant for this analysis Paste value in the code chunk below
To distinguish between isoforms or not (to use only generic UniprotACs): TRUE / FALSE? only isoforms = FALSE is relevant for this analysis Paste value in the code chunk below
Please specify the date for which you want to perform the analysis (if not today) “Logic table” from protein_properties script is needed for this analysis. Filename example:
“proteome_vs_interactome_protein_properties_f_Homo sapiens_reviewed_2_isoforms_FALSE_2016-12-01.txt”
the date of analysis, how old is Uniprot protein list: 2016-12-01
looking up species ID in the Uniprot readme file (always reads from url)
## [1] "UP000005640 9606 HUMAN 21032 71899 93381 Homo sapiens (Human)"
## Proteome_ID SPECIES_ID
## 1 UP000005640 9606
Reading SQL database for information about the disordered proteins
read the table saved before - script can be started from here
merge % of protein disordered to interaction data
## [1] "disorder NAs: 83"
## [1] "CIDER data NAs: 83"
## Warning: Ignoring unknown parameters: draw_quantiles, scale
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## Warning: Removed 24 rows containing non-finite values (stat_boxplot).
## Warning: Ignoring unknown parameters: draw_quantiles, scale
## Warning: Removed 2 rows containing non-finite values (stat_boxplot).
## Warning: Ignoring unknown parameters: draw_quantiles, scale
## Warning: Ignoring unknown parameters: draw_quantiles, scale
## Warning: Removed 114 rows containing non-finite values (stat_boxplot).
## Warning: Ignoring unknown parameters: draw_quantiles, scale
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Removed 107 rows containing non-finite values (stat_smooth).
## R version 3.3.2 (2016-10-31)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X El Capitan 10.11.6
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] MASS_7.3-45 scales_0.4.1 ggplot2_2.2.0 dplyr_0.5.0 RSQLite_1.1-1
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.8 knitr_1.15.1 magrittr_1.5 munsell_0.4.3
## [5] colorspace_1.3-1 R6_2.2.0 stringr_1.1.0 plyr_1.8.4
## [9] tools_3.3.2 grid_3.3.2 gtable_0.2.0 DBI_0.5-1
## [13] htmltools_0.3.5 yaml_2.1.14 lazyeval_0.2.0 assertthat_0.1
## [17] rprojroot_1.1 digest_0.6.10 tibble_1.2 memoise_1.0.0
## [21] evaluate_0.10 rmarkdown_1.2 labeling_0.3 stringi_1.1.2
## [25] backports_1.0.4